Chemistry

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Shiv Nadar University

Neutron crystallography is a powerful technique for experimental visualization of the positions of light atoms, including hydrogen and its isotope deuterium. In recent years, structural biologists have shown increasing interest in the technique as it uniquely complements X-ray crystallographic data by revealing the positions of D atoms in macromolecules. With this regained interest, access to macromolecular neutron crystallography beamlines is becoming a limiting step. In this report, it is shown that a rapid data-collection strategy can be a valuable alternative to longer data-collection times in appropriate cases. Comparison of perdeuterated rubredoxin structures refined against neutron data sets collected over hours and up to 5 d shows that rapid neutron data collection in just 14 h is sufficient to provide the positions of 269 D atoms without ambiguity. © 2012 International Union of Crystallography Printed in Singapore - all rights reserved.

(SoNS) School of Natural Sciences

World University root node

Acta Crystallographica Section D: Biological Crystallography

Rapid visualization of hydrogen positions in protein neutron crystallographic structures

Molecular docking methodology is useful in predicting comparative binding affinity of library of different ligands whose co-crystal structure in complex form is already known. However, scope of this methodology is not reliable for cross docking of different ligands due to incorrect prediction of binding pose if co-crystal structure is unknown. In the present work, we have studied the ligand polarization due to protein environment during the docking of seven ligands in envelope protein of dengue virus. We have used six kinase inhibitors which are active for dengue virus as well and a detergent molecule whose crystal structure is already known. We observed major change in docking scores due to polarization of ligands. The charges of the ligands were calculated by ab initio methods for the accuracy of our results. We observed increased hydrogen bonding due to polarization in protein environment. These results are more significant for inhibitors containing electronegative elements like chlorine and fluorine. © Springer Science+Business Media, LLC 2011.

Medicinal Chemistry Research

Role of polarization in ligand docking and binding affinity prediction for inhibitors of dengue virus

One of the most promising advantages of surface-enhanced Raman scattering (SERS) technique for in vivo biosensing is the multiplexing potential, which is under explored due to the limited availability of near-infrared Raman reporters. Here, we report the synthesis of multiplexing capable and biocompatible SERS nanotags using highly sensitive novel NIR Raman reporters. Two new NIR Raman reporter molecules, Cy7LA, Cy7.5LA are developed to partner with recently synthesized CyNAMLA-381 reporter to construct SERS nanotags with multiplexing capability. These nanotags possess excellent SERS signal stability over a period of one month. As a proof of concept for multiplex targeted in vivo detection, we successfully demonstrated the simultaneous sensing of cancer in living mouse using these three bioconjugated nanotags. To the best of our knowledge, this is the first real demonstration of in vivo multiplex targeted detection using SERS nanotags. Further, in vivo kinetic study of these nanotags in tumor revealed their excellent sensitivity, stability and tumor specificity. These probes also show rapid clearance from the liver indicating their possible excretion. This validation renders our SERS nanotags as an ultrasensitive in vivo nanoprobe for the detection and imaging of multiple biomarkers for early diagnosis of diseases. © 2012 Elsevier Ltd. All rights reserved.

Nano Today

Multiplex targeted in vivo cancer detection using sensitive near-infrared SERS nanotags

We demonstrate applications of quantitative structure-property relationship (QSPR) modeling to supplement first-principles computations in materials design. We have here focused on the design of polymers with specific electronic properties. We first show that common materials properties such as the glass transition temperature (T g) can be effectively modeled by QSPR to generate highly predictive models that relate polymer repeat unit structure to T g. Next, QSPR modeling is shown to supplement and guide first-principles density functional theory (DFT) computations in the design of polymers with specific dielectric properties, thereby leveraging the power of first-principles computations by providing high-throughput capability. Our approach consists of multiple rounds of validated MQSPR modeling and DFT computations to optimize the polymer skeleton as well as functional group substitutions thereof. Rigorous model validation protocols insure that the statistical models are able to make valid predictions on molecules outside the training set. Future work with inverse QSPRs has the potential to further reduce the time to optimize materials properties. © 2012 Springer Science+Business Media, LLC.

Fulltext

Journal of Materials Science

MQSPR modeling in materials informatics: A way to shorten design cycles?

The origins and significance of electron density in the chemical, biological, and materials sciences Electron density is one of the fundamental concepts underlying modern chemistry and one of the key determinants of molecular structure and stability. It is also the basic variable of density functional theory, which has made possible, in recent years, the application of the mathematical theory of quantum physics to chemical and biological systems. With an equal emphasis on computational and philosophical questions, A Matter of Density: Exploring the Electron Density Concept in the Chemical, Biological, and Materials Sciences addresses the foundations, analysis, and applications of this pivotal chemical concept. The first part of the book presents a coherent and logically connected treatment of the theoretical foundations of the electron density concept. Discussion includes the use of probabilities in statistical physics; the origins of quantum mechanics; the philosophical questions at the heart of quantum theory, like quantum entanglement; and methods for the experimental determination of electron density distributions. The remainder of the book deals with applications of the electron density concept in the chemical, biological, and materials sciences. Contributors offer insights on how a deep understanding of the origins of chemical reactivity can be gleaned from the concepts of density functional theory. Also discussed are the applications of electron density in molecular similarity analysis and electron density-derived molecular descriptors, such as electrostatic potentials and local ionization energies. This section concludes with some applications of modern density functional theory to surfaces and interfaces. An essential reference for students as well as quantum and computational chemists, physical chemists, and physicists, this book offers an unparalleled look at the development of the concept of electron density from its inception to its role in density functional theory, which led to the 1998 Nobel Prize in Chemistry. © 2013 John Wiley & Sons, Inc.

A Matter of Density: Exploring the Electron Density Concept in the Chemical, Biological, and Materials Sciences

Economics and Public Policy

(SME) School of Management and Entrepreneurship

Preface

A new class of thermoset polymers was synthesized based on agrochemical renewable cardanol-A by-product of cashew nut industry. A solventless synthesis of bisbenzoxazine monomers based on bisphenol-A (b) and aniline (abbreviated as Bzb-A) and cardanol (c) with diamines namely bis-(4-(4-Aminophenoxy)phenyl)ether (HP), bis-(3-(4- aminophenoxy)phenyl)ether (HM), 4,40-diaminodiphenylsulphone (DDS) and 2,2-bis(4-(4-Aminophenoxy)phenyl)propane (BA) was carried out. The benzoxazine monomers (Bzc-HP, Bzc-HM, Bzc-DDS and Bzc-BA) were characterized by 1HNMR and FTIR spectroscopy. The curing exotherm depended on the structure of themonomers. The onset curing temperature (To) was lowest for Bzb-A (460 K) and highest in Bzc-HM (518 K). The decomposition temperature for 5% mass loss (T5%) of resins followed the order PBzb-A<PBzc-DDS< PBzc-BA<PBzc-HM & PBzc-HP. The materials showed their potential as adhesives. Lap shear strength on steel plates followed the trend PBzc-DDS<PBzc-HM<PBzc-BA< PBzc-HP. © Akademiai Kiado, Budapest, Hungary 2011.

Journal of Thermal Analysis and Calorimetry

Cardanol-based bisbenzoxazines: Effect of structure on thermal behaviour

The formation of covalent C60 monolayers through [4+2] Diels-Alder cycloaddition between C60 and anthracene monolayers grafted onto a silicon oxide surface was investigated by ellipsometry, fluorescence and by atomic force microscopy. © 2011 The Royal Society of Chemistry.

Chemical Communications

Direct formation of fullerene monolayers using [4+2] Diels-Alder cycloaddition

Turning light: A crystalline fullerene material based on H-bonding interactions exhibits highly polarized fluorescence emission, whose angle of polarization can be turned using light (see picture). This process can be used to write optical information onto the material, which can be read through the polarization component of the luminescence emitted by the material. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Angewandte Chemie - International Edition

Controlling the emission polarization from single crystals using light: Towards photopolic materials

We report the synthesis and characterization of a novel NIR fluorescent deoxyglucose analogue, CyNE 2-DG. Experiments in different cell lines showed a preferential uptake of CyNE 2-DG in cancer cells and its effective competition with unlabeled d-glucose. Cell imaging experiments demonstrated the superior cell-permeability of CyNE 2-DG over the NIR standard IRDye 800CW 2-DG, and validated its application for cancer cell imaging in the NIR region. © The Royal Society of Chemistry 2011.